I remember an old Thor comic side story back in the 90's where Balder and Sif throw him into a never ending pit of monsters covered by a forceshield created by Hera. Destroyer could have destroyed the forcefield to get out, but the monsters kept fighting him endlessly.
So SS, Thor or Green Lantern could open some type of vortex into the Anti-matter universe or throw him into a black hole. Kinda cheap, but Destroyer would have a hell of a time trying to get out.
If they needed to literally destroy him by some plot device. Like a decree of the Celestials who were gonna wipe out a galaxy because of the threat that Destroyer could pose, than Destroyer takes it. Nothing I have seen has ever penetrated that armor. Hell, the only thing a full last-ditch Mjolnir force blast got the original Thor was a beating. You do not F with the Destroyer, you run away or you trick the damn thing.